i wouldnt mind having warning levels, where warnings are ranked in order of severity. then you have a minimum warning level at which a popup occures anything below that gets logged or tossed. i tend to like to get rid of the big problems first, then add the polish necessary to keep the debug warnings away. i might not fix a model thats scheduled to be replaced for example. when testing mods its common to have to run the game after each tweak many times. its just sort of a pita to have to click all those errors on a tweak/run cycle. there are ways to keep this from becoming a problem, like running retail builds.
then theres dealing with cutting edge builds, which might have features that you plan on using and other features in stable builds that you want/need to test as well. running under different builds tends to throw different errors depending on your usage of their various features. setting warning levels here would also come in handy, because the bugs technically arent there, the code just doesnt like running a feature thats in another build.
i find clicking through errors a hindrance to the modding process when i have no choice but to use a debug build. yes i know theres errors that need to be fixed, and yes i do fix those but in the latter stages of mod development, when all the placeholders have been removed and the tables refined for a particular target build (which in most cases hasnt even come out yet).